Through computation, this paper obtained Aflatoxin B1 and its trans-isomer molecules stable structure which was rarely reported by the density functional theory(DFT) with B3LYP complex function and 6-311+g(d, p) basis set. Through a single point calculations and geometry analysis, we know that the cis -structure is more stable than trans-structure. On the basis of this, Raman spectra of two molecules are calculated by the same method and basis set. compared with the Aflatoxin B1 cis -structure powder experimental Raman spectra, it was informed that numerical results with experimental results combined with a better. While 1 582, 3 065, 1 626 means to take the strongest of the three peaks of cis-structure raman characteristics, 1 616, 3 065, 1 659 cm-1 is indicated for the strongest of the three peaks of trans-structure raman characteristics. Use the Hirshfeld atom division method combined with Multiwfn software to analyze the composition of frontier orbital based on optimization calculation, and it was informed that the electrophilic ability of two m on olecules was stronger than the nucleophilic ability. The proportion of C1 atoms in LUMO orbital are respectively 21. 48 percent, 20. 62 percent by calculating, thus it is predicted that C1 atom is most main position spot depriving of the electronic in DNA to cause cancer. The above-mentioned research has certain theoretical directive significance in detection, transformation and toxicity inhibition of the cis-trans isomers.